Run initiated at 2024-06-11 11:45:24 BST

Report generated at 2024-07-05 17:18:32 BST

Input Parameters

  • input_dir: /home/amorris/BioInf/Parapipe_modtest/datasets/E2E/
  • output_dir: E2E_3
  • ref: cryptosporidium_parvum
  • yaml: false
  • db: false

    • Mapping Statistics

    Mapping statistics for samples within this Parapipe run.

    MultiQC report: /home/amorris/BioInf/PP_html_report_WD/e2e_data/multiqc_report.html

    Gini-Granularity Curves

    GG curves characterise coverage inequality. Low GG-area indicates low coverage equality. Low normalised GG-area indicates reads aggregate in small regions, whereas high normalised GG-area indicates reads aggregate in larger regions [1].

    Phylogenetic Analysis

    All analysis carried out using absolute (Hamming) SNP distance across the whole genome.

    Key:

    red = samples processed this run.

    grey = samples included in the input archive.

    SNP Report

    MOI Analysis

    HL1-2-3

    HL1-2

    HL1-3

    HL2-3

    L1.1

    L1.2

    L1.3

    L1.4

    L1.5

    L1

    L2.1

    L2.2

    L2.3

    L2.4

    L2.5

    L2

    L3.1

    L3.2

    L3.3

    L3.4

    L3.5

    L3